Sib-pair Command: list


ClassGlobal
Namelist | ls
Arguments[<loc1> [[to] <locN> [$(a|q|m|h|x|A|D)[m|r]]
where <search_string>
where position <map_pos1> [-- | to <map_pos2>] ...

List of loci in current analysis. The "$<letter>" keyword denotes the list of of one class of locus, which can be reordered according to genetic map position (m) or in reverse (r) to the dataset ordering (mr is by reverse map order). The modifiers do not affect A and D, which are the sets of all active and all inactive loci respectively.

$aAll active binary traits
$arAll active binary traits in reverse dataset order
$qAll active quantitative traits
$qrAll active quantitative traits in reverse dataset order
$mAll active codominant markers
$mrAll active codominant markers in reverse dataset order
$mmAll active codominant markers in map order
$mmrAll active codominant markers in reverse map order
$xAll active X-chromosomal markers
$xrAll active X-chromosomal markers in reverse dataset order
$xmAll active X-chromosomal markers in map order
$xmrAll active X-chromosomal markers in reverse map order
$hAll active haploid markers (Y or mitochondrial)
$hrAll active haploid markers in reverse dataset order
$hmAll active haploid markers in map order
$hmrAll active haploid markers in reverse map order
$AAll active loci
$DAll dropped loci

Loci can be referred to by their index in the list of loci (1..N).

Using list gives a full output with one line per locus, while ls gives an abbreviated output mimicking the results of the unix ls -F command.

The where modifier allows subsetting by an annotation matching a given search string or for a range of map positions. Map positions take the form <chr>:<coordinate> or chrXX <coordinate>. If a chromosome is not specified for a given map position, then the chromosome for the previous map position is used. A map interval may be open ended, in which case it extends to the end of the chromosome.

Example:

>> include williamsex.in

>> lis

Locus           Type Position
--------------- ---- ----------------
age              q         6
CHD              a         7
carrier          a         8
adjChol          q         9
ldl              m        10--     11

Number of marker loci=       1
Bonferroni corr. 5%  =    0.050000
Bonferroni corr. 1%  =    0.010000
Bonferroni corr. 0.1%=    0.001000

>> ls
age* CHD* carrier* adjChol* ldl
 4  active traits;  1  active markers.

>> ls $q
age* adjChol*
 2  active traits;  0  active markers.

>> ls $qr
adjChol* age*
 2  active traits;  0  active markers.

>> ls 1 2
age* CHD*
 2  active traits;  0  active markers.

>> ls carrier -- ldl
carrier* adjChol* ldl
 2  active traits;  1  active markers.

>> clear
>> include cavanaughex.in
>> lis whe pos 16:55.012
>> lis whe pos 16:54 -- 56
>> lis whe pos chr16 55.012
>> lis whe "26784604"
>> lis whe 267[789]*

[All give]

Locus        Type Position
------------ ---- ----------------
D16S3145      m         9--     10   26784604 (chr 16)

See also:

show locilocus information
whichlist positions of loci


<< (info)Up to index>> (which)